ALG6 c.*89G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.181%, nfe)
Conditions
1
ALG6-congenital disorder of glycosylation 1C
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.06 | GERP -2.8 |
| Non-coding constraint | Z 2.37 | 1 kb window · o/e 0.81 · regional · uncalibrated |
| Overall | ||
| CADD | 0.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.181%
European (non-Finnish) · 1,445/799,578 alleles
Filtering AF
0.173%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.17%
Overall
0.13%
1,505/1,155,956 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.181% | 553 |
| Remaining individualsnot grpmax-eligible | 0.0789% | 1,267 |
| African / African-American | 0.0246% | 4,061 |
| Finnishnot grpmax-eligible | 0.00806% | 12,403 |
| Admixed American | 0.00408% | 24,512 |
| East Asian | 0.00252% | 39,614 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ALG6
- Coding
- c.*89G>A
- MANE Select
- NM_013339
- dbSNP
- rs531808380
- Type
- single nucleotide variant
- Location
- chr1:63437109 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.08
Disease context
ALG6-congenital disorder of glycosylation 1C — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor ALG6-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- ALG6 c.1128-1G>A Likely pathogenic ★★ same condition
- ALG6 c.1128-2A>C Likely pathogenic ★★ same condition
- ALG6 c.1326+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ALG6 c.257+5G>A Pathogenic/Likely pathogenic ★★ same condition
- ALG6 c.429+1G>T Likely pathogenic ★★ same condition
- ALG6 c.495-2A>G Likely pathogenic ★★ same condition
- ALG6 c.495-2A>T Likely pathogenic ★★ same condition
- ALG6 c.680+1G>A Pathogenic/Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/alg6-c-star-89g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown